9DUO | pdb_00009duo

Human PELP1-WDR18 complex

  • Classification: STRUCTURAL PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2024-10-03 Released: 2025-04-30 
  • Deposition Author(s): Huang, J., Tong, L.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular insights into the overall architecture of human rixosome.

Huang, J.Tong, L.

(2025) Nat Commun 16: 3288-3288

  • DOI: https://doi.org/10.1038/s41467-025-58732-3
  • Primary Citation of Related Structures:  
    9DUM, 9DUN, 9DUO

  • PubMed Abstract: 

    Rixosome is a conserved, multi-subunit protein complex that has critical roles in ribosome biogenesis and silencing of Polycomb target genes. The subunits of human rixosome include PELP1, WDR18, TEX10, LAS1L and NOL9, with LAS1L providing the endoribonuclease activity and NOL9 the RNA 5' kinase activity. We report here cryo-EM structures of the human PELP1-WDR18-TEX10 and LAS1L-NOL9 complexes and a lower-resolution model of the human PELP1-WDR18-LAS1L complex. The structures reveal the overall organization of the human rixosome core scaffold of PELP1-WDR18-TEX10-LAS1L and indicate how the LAS1L-NOL9 endonuclease/kinase catalytic module is recruited to this core scaffold. Each TEX10 molecule has two regions of contact with WDR18, while the helix at the C terminus of WDR18 interacts with the helical domain of LAS1L. The structural observations are supported by our mutagenesis studies. Mutations in both WDR18-TEX10 contact regions can block the binding of TEX10, while truncation of the C-terminal helix of WDR18 can abolish the binding of LAS1L. The structures also reveal substantial conformational differences for TEX10 between the PELP1-WDR18-TEX10 complex alone and that in complex with pre-ribosome.


  • Organizational Affiliation
    • Department of Biological Sciences, Columbia University, New York, NY, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 18
A, B
434Homo sapiensMutation(s): 0 
Gene Names: WDR18
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BV38 (Homo sapiens)
Explore Q9BV38 
Go to UniProtKB:  Q9BV38
PHAROS:  Q9BV38
GTEx:  ENSG00000065268 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BV38
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proline-, glutamic acid- and leucine-rich protein 1
C, D
644Homo sapiensMutation(s): 0 
Gene Names: PELP1HMX3MNAR
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IZL8 (Homo sapiens)
Explore Q8IZL8 
Go to UniProtKB:  Q8IZL8
PHAROS:  Q8IZL8
GTEx:  ENSG00000141456 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IZL8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118093

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-28
    Changes: Data collection